$nTables = count($aTables);
// FIXME. remove later when TABLE_PATHOGENIC and TABLE_HITS are exterminated in all LOVD installations.
//print(' Found ' . $nTables . '/' . count($_TABLES) . ' tables.' . "\n");
$_TABLES_cleaned = $_TABLES;
unset($_TABLES_cleaned['TABLE_PATHOGENIC']);
unset($_TABLES_cleaned['TABLE_HITS']);
print ' Found ' . $nTables . '/' . count($_TABLES_cleaned) . ' tables.' . "\n";
// FIXME; add more later.
// General statistics...
print "\n";
// 2012-02-01; 3.0-beta-02; Exclude "LOVD" system user.
$nUsers = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_USERS . ' WHERE id > 0')->fetchColumn();
$nIndividuals = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_INDIVIDUALS)->fetchColumn();
$nScreenings = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_SCREENINGS)->fetchColumn();
$nVars = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_VARIANTS)->fetchColumn();
$nGenes = count(lovd_getGeneList());
print ' Found ' . $nUsers . ' user' . ($nUsers == 1 ? '' : 's') . '.' . "\n" . ' Found ' . $nIndividuals . ' individual' . ($nIndividuals == 1 ? '' : 's') . '.' . "\n" . ' Found ' . $nScreenings . ' screening' . ($nScreenings == 1 ? '' : 's') . '.' . "\n" . ' Found ' . $nVars . ' variant' . ($nVars == 1 ? '' : 's') . '.' . "\n" . ' Found ' . $nGenes . ' gene' . ($nGenes == 1 ? '' : 's') . '.' . "\n" . ' </PRE>' . "\n";
if ($nGenes || $nIndividuals || $nVars) {
lovd_showInfoTable('FINAL WARNING! If you did not download the variation and individual data stored in the LOVD system, everything will be lost!', 'warning');
}
print ' Please confirm uninstalling LOVD using your password.<BR>' . "\n" . ' <BR>' . "\n\n";
}
lovd_errorPrint();
print ' <FORM action="' . $_PE[0] . '?confirm" method="post">' . "\n" . ' <TABLE border="0" cellpadding="0" cellspacing="0" width="300">' . "\n" . ' <TR align="right">' . "\n" . ' <TD width="125" style="padding-right : 5px;">Password</TD>' . "\n" . ' <TD width="175"><INPUT type="password" name="password" size="20"></TD></TR>' . "\n" . ' <TR align="right">' . "\n" . ' <TD width="125"> </TD>' . "\n" . ' <TD width="175"><INPUT type="submit" value="Uninstall LOVD" style="font-weight : bold; font-size : 11px; width : 110px;"></TD></TR></TABLE></FORM>' . "\n\n";
$_T->printFooter();
exit;
}
}
if (empty($_POST)) {
print ' Welcome to the LOVD uninstaller. Please continue by providing your password.<BR>' . "\n" . ' <BR>' . "\n\n";
lovd_showInfoTable('WARNING! If you did not download your data, you will lose all of it!', 'warning');
}
}
if ($aToRemove) {
$q = $_DB->query('DELETE FROM ' . TABLE_SCR2GENE . ' WHERE screeningid = ? AND geneid IN (?' . str_repeat(', ?', count($aToRemove) - 1) . ')', array_merge(array($zData['id']), $aToRemove), false);
if (!$q) {
// Silent error.
lovd_writeLog('Error', LOG_EVENT, 'Gene information entr' . (count($aToRemove) == 1 ? 'y' : 'ies') . ' ' . implode(', ', $aToRemove) . ' could not be removed from screening ' . $nID);
} else {
lovd_writeLog('Event', LOG_EVENT, 'Gene information entr' . (count($aToRemove) == 1 ? 'y' : 'ies') . ' ' . implode(', ', $aToRemove) . ' successfully removed from screening ' . $nID);
}
}
// Add genes.
$aSuccess = array();
$aFailed = array();
foreach ($_POST['genes'] as $sGene) {
if (!in_array($sGene, $zData['genes']) && in_array($sGene, lovd_getGeneList())) {
// Add gene to screening.
$q = $_DB->query('INSERT IGNORE INTO ' . TABLE_SCR2GENE . ' VALUES (?, ?)', array($nID, $sGene), false);
if (!$q) {
$aFailed[] = $sGene;
} else {
$aSuccess[] = $sGene;
}
}
}
// Get genes which are modified only when linked variant is marked or public.
$aGenes = $_DB->query('SELECT DISTINCT t.geneid FROM ' . TABLE_TRANSCRIPTS . ' AS t ' . 'INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (vot.transcriptid = t.id) ' . 'INNER JOIN ' . TABLE_VARIANTS . ' AS vog ON (vog.id = vot.id) ' . 'INNER JOIN ' . TABLE_SCR2VAR . ' AS s2v ON (s2v.variantid = vog.id) ' . 'INNER JOIN ' . TABLE_SCREENINGS . ' AS s ON (s.id = s2v.screeningid) ' . 'INNER JOIN ' . TABLE_INDIVIDUALS . ' AS i ON (i.id = s.individualid) ' . 'WHERE vog.statusid >= ? AND i.statusid >= ? AND s2v.screeningid = ?', array(STATUS_MARKED, STATUS_MARKED, $nID))->fetchAllColumn();
if ($aGenes) {
// Change updated date for genes
lovd_setUpdatedDate($aGenes);
}
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* LOVD is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with LOVD. If not, see <http://www.gnu.org/licenses/>.
*
*************/
define('ROOT_PATH', '../');
require ROOT_PATH . 'inc-init.php';
session_write_close();
$aGenes = lovd_getGeneList();
if (empty($_GET['variant']) || !preg_match('/^([A-Z]{2}_\\d{6,9}\\.\\d{1,2}(\\([A-Za-z0-9-]+_v\\d{3}\\))?:[cn])|(chr.{0,2}:[gm])\\..+$/', $_GET['variant']) || empty($_GET['gene']) || !in_array($_GET['gene'], $aGenes)) {
die(AJAX_DATA_ERROR);
}
// Requires at least LEVEL_SUBMITTER, anything lower has no $_AUTH whatsoever.
if (!$_AUTH) {
// If not authorized, die with error message.
die(AJAX_NO_AUTH);
}
require ROOT_PATH . 'class/soap_client.php';
$_Mutalyzer = new LOVD_SoapClient();
$sGene = $_GET['gene'];
// If the gene is defined in the mito_genes_aliases in inc-init.php, use the NCBI gene symbol.
if (isset($_SETT['mito_genes_aliases'][$_GET['gene']])) {
$sGene = $_SETT['mito_genes_aliases'][$_GET['gene']];
}
function lovd_checkDBID($aData)
{
// Checks if given variant and DBID match. I.e., whether or not there is
// already an entry where this variant and DBID come together.
// NOTE: We're assuming that the DBID field actually exists. Using this
// function implies you've checked for it's presence.
// All checks ignore the current variant, if the ID is given.
global $_DB;
// <chr||GENE>_000000 is always allowed.
$sSymbol = substr($aData['VariantOnGenome/DBID'], 0, strpos($aData['VariantOnGenome/DBID'], '_'));
$sGenomeVariant = str_replace(array('(', ')', '?'), '', $aData['VariantOnGenome/DNA']);
if (!isset($aData['aTranscripts'])) {
$aData['aTranscripts'] = array();
}
$aTranscriptVariants = array();
if (!empty($aData['aTranscripts'])) {
$aGenes = array();
foreach ($aData['aTranscripts'] as $nTranscriptID => $aTranscript) {
// Check for non-empty VariantOnTranscript/DNA fields for each transcript and return true immediately when GENE_000000 is used.
$aGenes[] = $aTranscript[1];
if (!empty($aData[$nTranscriptID . '_VariantOnTranscript/DNA'])) {
$aTranscriptVariants[$nTranscriptID] = str_replace(array('(', ')', '?'), '', $aData[$nTranscriptID . '_VariantOnTranscript/DNA']);
}
if (!isset($aData['ignore_' . $nTranscriptID]) && $aData['VariantOnGenome/DBID'] == $aTranscript[1] . '_000000') {
return true;
}
}
}
if ($aData['VariantOnGenome/DBID'] == 'chr' . $aData['chromosome'] . '_000000') {
// Check if chr_000000 is used and return true if this is the case.
return true;
}
$nIDtoIgnore = !empty($aData['id']) ? $aData['id'] : 0;
// Check if the DBID entered is already in use by a variant entry excluding the current one.
$nHasDBID = $_DB->query('SELECT COUNT(id) FROM ' . TABLE_VARIANTS . ' WHERE `VariantOnGenome/DBID` = ? AND id != ?', array($aData['VariantOnGenome/DBID'], $nIDtoIgnore))->fetchColumn();
if ($nHasDBID && (!empty($sGenomeVariant) || !empty($aTranscriptVariants))) {
// This is the standard query that will be used to determine if the DBID given is correct.
$sSQL = 'SELECT DISTINCT t.geneid, ' . 'CONCAT(IFNULL(vog.`VariantOnGenome/DNA`, ""), ";", IFNULL(GROUP_CONCAT(vot.`VariantOnTranscript/DNA` SEPARATOR ";"), "")) as variants, ' . 'vog.`VariantOnGenome/DBID` ' . 'FROM ' . TABLE_VARIANTS . ' AS vog LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (vog.id = vot.id) ' . 'LEFT OUTER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) ' . 'WHERE (';
$aArgs = array();
$sWhere = '';
if (!empty($sGenomeVariant)) {
// SQL addition to check the genomic notation-chromosome combination.
$sWhere .= '(REPLACE(REPLACE(REPLACE(vog.`VariantOnGenome/DNA`, "(", ""), ")", ""), "?", "") = ? AND vog.chromosome = ?) ';
$aArgs[] = $sGenomeVariant;
$aArgs[] = $aData['chromosome'];
}
foreach ($aTranscriptVariants as $nTranscriptID => $sTranscriptVariant) {
// SQL addition to check the transcript notation-transcript combination.
$sWhere .= (!empty($sWhere) ? 'OR ' : '') . '(REPLACE(REPLACE(REPLACE(vot.`VariantOnTranscript/DNA`, "(", ""), ")", ""), "?", "") = ? AND vot.transcriptid = ?) ';
$aArgs[] = $sTranscriptVariant;
$aArgs[] = $nTranscriptID;
}
// SQL addition to check if the above combinations are found with the given DBID.
$sWhere .= ') AND BINARY vog.`VariantOnGenome/DBID` = ? ';
$aArgs[] = $aData['VariantOnGenome/DBID'];
if ($nIDtoIgnore > 0) {
// SQL addition to exclude the current variant, where the $aData belongs to.
$sWhere .= 'AND vog.id != ? ';
$aArgs[] = sprintf('%010d', $nIDtoIgnore);
}
$sSQL .= $sWhere . 'GROUP BY vog.id';
$aOutput = $_DB->query($sSQL, $aArgs)->fetchAllRow();
$nOptions = count($aOutput);
if (!$nOptions) {
return false;
}
} elseif (!empty($aGenes) && !in_array($sSymbol, $aGenes)) {
// VOT, but DBID does not use the gene symbol of one of these VOT's.
return false;
} elseif (empty($aGenes)) {
// VOG
if (substr($aData['VariantOnGenome/DBID'], 0, 3) != 'chr') {
if (!in_array($sSymbol, lovd_getGeneList())) {
// Gene symbol used in the DBID does not exist in the database.
return false;
}
} elseif ($sSymbol != 'chr' . $aData['chromosome']) {
// Chromosome number in the DBID does not match the chromosome of the genomic variant.
return false;
}
}
return true;
}
